data_2LJ # _chem_comp.id 2LJ _chem_comp.name "1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H20 N4 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "5-(2-oxopropylideneamino)-6-D-ribitylaminouracil" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-11-27 _chem_comp.pdbx_modified_date 2024-09-27 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 316.310 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2LJ _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 6MWR _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal 2LJ C4 C1 C 0 1 N N N N N N 9.157 14.141 37.680 -3.914 0.723 -0.181 C4 2LJ 1 2LJ C6 C2 C 0 1 N N N N N N 7.755 11.559 37.330 -3.476 -2.142 -0.047 C6 2LJ 2 2LJ C7 C3 C 0 1 N N N N N N 7.107 10.252 37.184 -3.564 -3.577 -0.501 C7 2LJ 3 2LJ C8 C4 C 0 1 N N N N N N 5.677 10.201 36.720 -3.255 -4.504 0.676 C8 2LJ 4 2LJ N1 N1 N 0 1 N N N N N N 8.152 16.030 35.833 -1.537 2.014 0.241 N1 2LJ 5 2LJ N3 N2 N 0 1 N N N N N N 9.533 15.473 37.631 -3.882 2.025 0.163 N3 2LJ 6 2LJ N5 N3 N 0 1 N N N N N N 7.530 12.517 36.503 -2.700 -1.316 -0.666 N5 2LJ 7 2LJ C4A C5 C 0 1 N N N N N N 8.154 13.755 36.656 -2.698 0.010 -0.321 C4A 2LJ 8 2LJ O4 O1 O 0 1 N N N N N N 9.643 13.407 38.540 -4.980 0.162 -0.365 O4 2LJ 9 2LJ C2 C6 C 0 1 N N N N N N 9.077 16.433 36.763 -2.712 2.655 0.369 C2 2LJ 10 2LJ O2 O2 O 0 1 N N N N N N 9.448 17.600 36.838 -2.716 3.832 0.674 O2 2LJ 11 2LJ C8A C7 C 0 1 N N N N N N 7.683 14.753 35.753 -1.501 0.686 -0.102 C8A 2LJ 12 2LJ N8 N4 N 0 1 N N N N N N 6.698 14.493 34.893 -0.303 0.035 -0.232 N8 2LJ 13 2LJ "C1'" C8 C 0 1 N N N N N N 5.929 15.411 34.067 0.951 0.757 -0.005 "C1'" 2LJ 14 2LJ "C2'" C9 C 0 1 N N S N N N 6.351 15.503 32.601 2.132 -0.193 -0.213 "C2'" 2LJ 15 2LJ "O2'" O3 O 0 1 N N N N N N 6.466 14.201 32.024 2.035 -1.282 0.708 "O2'" 2LJ 16 2LJ "C3'" C10 C 0 1 N N S N N N 7.653 16.287 32.415 3.441 0.560 0.024 "C3'" 2LJ 17 2LJ "O3'" O4 O 0 1 N N N N N N 7.668 17.438 33.253 3.538 1.649 -0.896 "O3'" 2LJ 18 2LJ "C4'" C11 C 0 1 N N R N N N 7.970 16.699 30.975 4.622 -0.390 -0.184 "C4'" 2LJ 19 2LJ "O4'" O5 O 0 1 N N N N N N 9.341 17.091 30.897 4.525 -1.479 0.737 "O4'" 2LJ 20 2LJ "C5'" C12 C 0 1 N N N N N N 7.092 17.823 30.413 5.932 0.363 0.054 "C5'" 2LJ 21 2LJ "O5'" O6 O 0 1 N N N N N N 7.483 18.170 29.091 7.036 -0.491 -0.253 "O5'" 2LJ 22 2LJ H1 H1 H 0 1 N N N N N N 8.437 11.721 38.151 -4.062 -1.806 0.795 H1 2LJ 23 2LJ H2 H2 H 0 1 N N N N N N 7.146 9.760 38.167 -4.570 -3.780 -0.870 H2 2LJ 24 2LJ H3 H3 H 0 1 N N N N N N 7.702 9.675 36.461 -2.843 -3.750 -1.300 H3 2LJ 25 2LJ H4 H4 H 0 1 N N N N N N 5.346 9.153 36.664 -3.977 -4.331 1.474 H4 2LJ 26 2LJ H5 H5 H 0 1 N N N N N N 5.041 10.749 37.431 -3.319 -5.542 0.347 H5 2LJ 27 2LJ H6 H6 H 0 1 N N N N N N 5.598 10.664 35.725 -2.250 -4.301 1.044 H6 2LJ 28 2LJ H7 H7 H 0 1 N N N N N N 10.212 15.768 38.303 -4.713 2.515 0.262 H7 2LJ 29 2LJ H9 H9 H 0 1 N N N N N N 6.010 14.019 35.442 -0.285 -0.904 -0.475 H9 2LJ 30 2LJ H10 H10 H 0 1 N N N N N N 6.018 16.415 34.507 1.025 1.587 -0.707 H10 2LJ 31 2LJ H11 H11 H 0 1 N N N N N N 4.877 15.090 34.095 0.969 1.141 1.015 H11 2LJ 32 2LJ H12 H12 H 0 1 N N N N N N 5.561 16.052 32.068 2.113 -0.578 -1.233 H12 2LJ 33 2LJ H13 H13 H 0 1 N N N N N N 5.652 13.727 32.147 2.045 -1.014 1.637 H13 2LJ 34 2LJ H14 H14 H 0 1 N N N N N N 8.468 15.623 32.738 3.460 0.944 1.044 H14 2LJ 35 2LJ H15 H15 H 0 1 N N N N N N 7.471 17.182 34.147 3.528 1.380 -1.825 H15 2LJ 36 2LJ H16 H16 H 0 1 N N N N N N 7.819 15.815 30.339 4.604 -0.774 -1.204 H16 2LJ 37 2LJ H17 H17 H 0 1 N N N N N N 9.889 16.397 31.244 4.535 -1.211 1.666 H17 2LJ 38 2LJ H18 H18 H 0 1 N N N N N N 7.186 18.708 31.059 5.965 1.245 -0.587 H18 2LJ 39 2LJ H19 H19 H 0 1 N N N N N N 6.044 17.488 30.401 5.990 0.671 1.098 H19 2LJ 40 2LJ H20 H20 H 0 1 N N N N N N 6.924 18.867 28.768 7.900 -0.078 -0.125 H20 2LJ 41 2LJ H8 H8 H 0 1 N N N N N N 7.805 16.706 35.183 -0.708 2.494 0.391 H8 2LJ 42 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 2LJ "O5'" "C5'" SING N N 1 2LJ "C5'" "C4'" SING N N 2 2LJ "O4'" "C4'" SING N N 3 2LJ "C4'" "C3'" SING N N 4 2LJ "O2'" "C2'" SING N N 5 2LJ "C3'" "C2'" SING N N 6 2LJ "C3'" "O3'" SING N N 7 2LJ "C2'" "C1'" SING N N 8 2LJ "C1'" N8 SING N N 9 2LJ N8 C8A SING N N 10 2LJ C8A N1 SING N N 11 2LJ C8A C4A DOUB N N 12 2LJ N1 C2 SING N N 13 2LJ N5 C4A SING N N 14 2LJ N5 C6 DOUB N N 15 2LJ C4A C4 SING N N 16 2LJ C8 C7 SING N N 17 2LJ C2 O2 DOUB N N 18 2LJ C2 N3 SING N N 19 2LJ C7 C6 SING N N 20 2LJ N3 C4 SING N N 21 2LJ C4 O4 DOUB N N 22 2LJ C6 H1 SING N N 23 2LJ C7 H2 SING N N 24 2LJ C7 H3 SING N N 25 2LJ C8 H4 SING N N 26 2LJ C8 H5 SING N N 27 2LJ C8 H6 SING N N 28 2LJ N3 H7 SING N N 29 2LJ N8 H9 SING N N 30 2LJ "C1'" H10 SING N N 31 2LJ "C1'" H11 SING N N 32 2LJ "C2'" H12 SING N N 33 2LJ "O2'" H13 SING N N 34 2LJ "C3'" H14 SING N N 35 2LJ "O3'" H15 SING N N 36 2LJ "C4'" H16 SING N N 37 2LJ "O4'" H17 SING N N 38 2LJ "C5'" H18 SING N N 39 2LJ "C5'" H19 SING N N 40 2LJ "O5'" H20 SING N N 41 2LJ N1 H8 SING N N 42 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor 2LJ SMILES ACDLabs 12.01 "C1(=O)NC(NC(=C1\N=C\CC)NCC(O)C(O)C(O)CO)=O" 2LJ InChI InChI 1.03 "InChI=1S/C12H20N4O6/c1-2-3-13-8-10(15-12(22)16-11(8)21)14-4-6(18)9(20)7(19)5-17/h3,6-7,9,17-20H,2,4-5H2,1H3,(H3,14,15,16,21,22)/b13-3+/t6-,7+,9-/m0/s1" 2LJ InChIKey InChI 1.03 YCMPUNANLDFPQG-FHZGFTDOSA-N 2LJ SMILES_CANONICAL CACTVS 3.385 "CCC=NC1=C(NC[C@H](O)[C@H](O)[C@H](O)CO)NC(=O)NC1=O" 2LJ SMILES CACTVS 3.385 "CCC=NC1=C(NC[CH](O)[CH](O)[CH](O)CO)NC(=O)NC1=O" 2LJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC/C=N/C1=C(NC(=O)NC1=O)NC[C@@H]([C@@H]([C@@H](CO)O)O)O" 2LJ SMILES "OpenEye OEToolkits" 2.0.6 "CCC=NC1=C(NC(=O)NC1=O)NCC(C(C(CO)O)O)O" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier 2LJ "SYSTEMATIC NAME" ACDLabs 12.01 "1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol" 2LJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "5-[(~{E})-propylideneamino]-6-[[(2~{S},3~{S},4~{R})-2,3,4,5-tetrakis(oxidanyl)pentyl]amino]-1~{H}-pyrimidine-2,4-dione" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 2LJ "Create component" 2013-11-27 RCSB 2LJ "Initial release" 2014-04-16 RCSB 2LJ "Modify leaving atom flag" 2018-11-02 RCSB 2LJ "Modify value order" 2019-01-09 RCSB 2LJ "Modify synonyms" 2021-03-01 PDBE 2LJ "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 2LJ _pdbx_chem_comp_synonyms.name "5-(2-oxopropylideneamino)-6-D-ribitylaminouracil" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 2LJ _pdbx_chem_comp_pcm.modified_residue_id LYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C7 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #